The motion also says the February arrests of Lynn, three current and former priests, and a former teacher led new accusers to come forward, and identified claims against two priests who never before had been publicly accused of misconduct.
The filing is expected to launch a legal battle that could shape Lynn's trial, scheduled for March.
As secretary of clergy from 1992 until 2004, Lynn's job included investigating sex-abuse allegations against local priests. He also recommended to Cardinal Anthony J. Bevilacqua where to assign priests, including those accused of child sexual abuse.
Lynn is charged with conspiracy and child endangerment related to the rape of two altar boys in the 1990s. Charged with assault are the Revs. Charles Engelhardt and James Brennan, former priest Edward Avery, and onetime teacher Bernard Shero.
All have pleaded not guilty.
Lynn's lawyers, Jeffrey Lindy and Thomas Bergstrom, declined to comment on the filing, as did prosecutors. All cited a gag order by Common Pleas Court Judge M. Teresa Sarmina. Defense lawyers plan to file a response next month.
His lawyers have suggested that prosecutors are unfairly trying to bring against him the criminal case they chose not to pursue six years ago, when a grand jury first vilified the archdiocese over clergy sex abuse.
State rules regarding criminal evidence generally bar prosecutors from telling jurors about a defendant's prior record or other "bad acts" that might reflect on his character. An exception occurs when the evidence is offered to explain a defendant's motives, knowledge, and intent, or to show his actions were consistent with a pattern.
In their motion, prosecutors acknowledge that their case against Lynn could hinge on the past allegations.
"Without the context of the archdiocese's decades-long policy of protecting sexual offenders and Lynn's active participation in implementing this policy for over 10 years," Sorensen wrote, "his recommendations and actions on behalf of Avery and Brennan could mistakenly be viewed as something less than criminal."
Much of the 53-page motion filed Friday repeats decades-old claims of abuse and cover-up detailed in the 2005 grand jury report.
But the motion also includes allegations against two priests never before publicly accused of misconduct. In those cases, prosecutors say, Lynn not only failed to properly respond to allegations but admonished priests who brought the concerns to light.
In 1995, the motion says, a priest at St. Anselm in Northeast Philadelphia found a hoard of pornography in the bedroom of the Rev. Michael Murtha. One of the videos portrayed "an adult male whipping a naked young boy."
The collection also included a sexually explicit and handwritten love letter that Murtha had addressed to a seventh-grade altar boy, prosecutors say. It allegedly outlined Murtha's fantasies and ended by proposing a sex act with the boy, inviting him to respond by writing "the word yes on a real small piece of paper and stick it behind the border on the [school] bulletin board that has the student pictures of the week on it."
The motion does not say if Murtha sent the letter or had contact with the boy. It says he later admitted the materials were his and was sent to St. John Vianney, the archdiocesan-owned Downingtown hospital, for treatment.
Now 51, Murtha was listed on the archdiocese's directory of priests as recently as 2008 but is no longer associated with a parish. The motion says Cardinal Justin Rigali asked the Vatican to defrock Murtha last year.
Murtha could not be reached for comment. The archdiocese did not reply to a request about his status.
According to the motion, Lynn and Murtha agreed in 1996 to tell parishioners at St. Anselm that Murtha was being hospitalized for "high blood pressure and weight control."
Lynn also allegedly told Murtha that he did not "condone" the behavior of the Rev. Joseph Okonski, who alerted superiors to the pornography cache, and that he would impress upon Okonski the need "to maintain confidentiality."
Okonski, the pastor of St. Athanasius in Philadelphia, did not respond to messages left at his parish Friday.
In a second case, prosecutors say Lynn punished now-Mgsr. Michael Picard after he raised concerns in 1996 about "troubling conduct" by another priest, the Rev. Donald Mills, who was being transferred to Picard's parish, St. Andrew in Newtown, Bucks County.
The motion does not specify Mills' alleged conduct, but says Lynn dismissed the concerns as "hearsay" and "rumors," and then recommended that Picard be denied more staffing at his parish and be disciplined for disobedience.
Picard then waited 15 years to be promoted to monsignor. When it happened, Lynn allegedly told him, "Everybody deserves to get out of the penalty box at some point."
Mills died in 2006, a year after he was accused of sexually assaulting a minor in 1982.
Reached at his rectory Friday, Picard declined to comment.
The motion notes that this year's grand jury report prompted new complaints against two of the defendants. Since February, officials have lodged two new accusations of sexual misconduct against Avery, who was defrocked in 2006.
Prosecutors also outlined more complaints of touching or inappropriate behavior around students by Shero, who was a teacher at St. Jerome's in Northeast Philadelphia and other schools in the archdiocese. Nothing in the motion suggests that the allegations will fall within the statute of limitations or lead to new charges.
Contact staff writer John P. Martin at 215-854-4774, email@example.com, or @JPMartinInky on Twitter.